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Use sqlite .coverage file to do cool stuff #7

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50e2f82
Use SQLite file for getting coverage info as an alternative
spookylukey Jul 4, 2022
ce789e0
Check SQLite database version when opening
spookylukey Jul 6, 2022
4122e67
Function to extract context information for a path/line number
spookylukey Jul 6, 2022
b73eb39
Added command to rerun pytest tests based on context info
spookylukey Jul 7, 2022
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13 changes: 8 additions & 5 deletions README.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -43,10 +43,12 @@ Run ``flycheck-select-checker``, pick ``python-coverage``.
Coverage data
=============

This package reads the XML output produced by Python's ``coverage``
package. Usually this file is named ``coverage.xml``.
This package can read both the SQLite ``.coverage`` file created by Python’s
``coverage`` package, and the XML report it produces. The latter is preferred if
present, because the ``coverage xml`` command does some additional analysis to
ignore docstrings etc.

With plain `coverage`:
With plain ``coverage``, generate the XML file like this:

.. code-block:: shell

Expand All @@ -61,7 +63,7 @@ With ``pytest-cov``, pass ``--cov-report=xml``, e.g. via ``pyproject.toml``:
"--cov=your-package",
"--cov=test",
"--cov-report=xml",
]


Customization
=============
Expand All @@ -73,7 +75,8 @@ Command for manual coverage file selection:
Customizable settings (see their description for details) in the
``python-coverage`` group, e.g. via ``M-x customize-group``:

- ``python-coverage-default-file-name``
- ``python-coverage-default-xml-file-name``
- ``python-coverage-default-sqlite-file-name``
- ``python-coverage-overlay-width``

Styling via custom faces, e.g. via ``M-x customize-face``:
Expand Down
204 changes: 190 additions & 14 deletions python-coverage.el
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Expand Up @@ -21,16 +21,23 @@
(require 'filenotify)
(require 'python)
(require 's)
(require 'sqlite3)
(require 'xml)
(require 'xml+)
(require 'cl-lib)

(defgroup python-coverage nil
"Python coverage"
:group 'python
:prefix "python-coverage")

(defcustom python-coverage-default-file-name "coverage.xml"
"Default file name to use when looking for coverage results."
(defcustom python-coverage-default-xml-file-name "coverage.xml"
"Default file name to use when looking for coverage XML report."
:group 'python-coverage
:type 'string)

(defcustom python-coverage-default-sqlite-file-name ".coverage"
"Default file name to use when looking for coverage SQLite file."
:group 'python-coverage
:type 'string)

Expand Down Expand Up @@ -143,28 +150,70 @@ This is only needed if autodetection does not work."
"Obtain coverage info for the current buffer."
(-when-let*
((coverage-file (python-coverage--find-coverage-file-current-buffer))
(non-empty? (> (python-coverage--file-size coverage-file) 0))
(tree (python-coverage--parse-coverage-xml-file coverage-file))
(coverage-info (python-coverage--get-missing-file-coverage tree (buffer-file-name))))
coverage-info))
(non-empty? (> (python-coverage--file-size coverage-file) 0)))
;; Prefer XML because coveragepy includes some analysis about blank lines,
;; docstrings etc.
(if (python-coverage--is-xml coverage-file)
(-when-let
(tree (python-coverage--parse-coverage-xml-file coverage-file))
(python-coverage--get-missing-file-coverage tree (buffer-file-name)))
(python-coverage--query-missing-file-coverage coverage-file (buffer-file-name)))))

(defun python-coverage-rerun-pytest-current-region ()
"Re-run the relevant pytest tests accoring to recorded 'context' information.
This requires that pytest was run with --cov-context=test previously.
Current region or current line in current buffer is used."
(interactive)
(-when-let*
((coverage-file (python-coverage--find-coverage-file-current-buffer t))
(python-file-name (buffer-file-name))
(line-nums (if (region-active-p)
(apply 'number-sequence
(sort (list (line-number-at-pos (mark))
(line-number-at-pos (point)))
'<))
(list (line-number-at-pos (point)))))
(contexts (or (python-coverage--query-coverage-contexts coverage-file python-file-name line-nums)
(error "No related test contexts found for current region"))))
;; In pytest, test contexts look like this:
;;
;; path/to/src/module.py::TestClassName::test_method_name|run
;;
;; The last part can also be `setup` or `teardown`. For now, we assume that
;; any of these could be relevant.
;; (print (mapcar (lambda (item) (car (s-split "\|" item))) contexts))))
(-let [file-test-args (mapcar (lambda (item) (car (s-split "\|" item))) contexts)]
(print "Contexts:")
(print contexts)
(print "File test args:")
(print file-test-args)
(python-pytest--run
:args file-test-args
:edit current-prefix-arg))))

;; Internal helpers for handling files

(defun python-coverage--find-coverage-file-current-buffer ()
(defun python-coverage--find-coverage-file-current-buffer (&optional sqlite-only)
"Find a coverage file for the current buffer."
(-let [source-file-name
(or (buffer-file-name)
(error "Cannot detect source file name; buffer is not visiting a file"))]
(python-coverage--find-coverage-file source-file-name)))
(python-coverage--find-coverage-file source-file-name sqlite-only)))

(defun python-coverage--find-coverage-file (source-file-name)
(defun python-coverage--find-coverage-file (source-file-name &optional sqlite-only)
"Find a coverage file for SOURCE-FILE-NAME."
(or
python-coverage--coverage-file-name
(-some->
(python-coverage--locate-dominating-file source-file-name python-coverage-default-file-name)
(file-name-as-directory)
(s-concat python-coverage-default-file-name))
(or
(when (not sqlite-only)
(-some->
(python-coverage--locate-dominating-file source-file-name python-coverage-default-xml-file-name)
(file-name-as-directory)
(s-concat python-coverage-default-xml-file-name)))
(-some->
(python-coverage--locate-dominating-file source-file-name python-coverage-default-sqlite-file-name)
(file-name-as-directory)
(s-concat python-coverage-default-sqlite-file-name)))
(error "Could not find coverage file. (Hint: use ‘M-x python-coverage-select-coverage-file’ to choose manually.)")))

(declare-function projectile-locate-dominating-file "projectile" (file name))
Expand Down Expand Up @@ -196,8 +245,132 @@ FILE and NAME are handled like ‘locate-dominating-file’ does."
(->> (file-attributes file-name)
(nth 7)))

;; Internal helpers for handling the SQLite coverage format

(defun python-coverage--query-missing-file-coverage (coverage-file python-file-name)
(-when-let*
((dbh-version (python-coverage--open-coverage-db coverage-file))
(dbh (car dbh-version))
;; Use hex() for the BLOB data because the sqlite3 bindings don't
;; seem to have another way to pass binary data through.
(stmt (sqlite3-prepare dbh "
SELECT DISTINCT hex(numbits)
FROM line_bits
INNER JOIN file ON line_bits.file_id = file.id
WHERE path = ?")))
(sqlite3-bind-text stmt 1 python-file-name)
(let* ((nums ()))
(while (= sqlite-row (sqlite3-step stmt))
(-let
[(hex-numbits) (sqlite3-fetch stmt)]
(setq nums (cl-nunion nums (python-coverage--hex-numbits-to-nums hex-numbits)))))
(sqlite3-finalize stmt)
(sqlite3-close dbh)

;; Convert the 'hits=1' lines we've got into 'missing' lines.
;; We reproduce a little bit of the analysis done by coveragepy:
;; - empty lines shouldn't count as missing
(with-temp-buffer
(insert-file-contents python-file-name)
(let* ((line-count (count-lines (point-min) (point-max)))
(empty-source-lines (python-coverage--get-empty-source-lines))
(missing-lines
(cl-set-difference (number-sequence 1 (+ 1 line-count))
(cl-nunion nums empty-source-lines))))
(python-coverage--merge-adjacent
(mapcar (lambda (num)
(list :line-beg num :line-end num :status 'missing))
missing-lines)))))))


(defun python-coverage--query-coverage-contexts (coverage-file python-file-name line-nums)
"Use the SQLite coverage database COVERAGE-FILE to get the contexts that cover PYTHON-FILE-NAME lines LINE-NUMS"
(-when-let*
((dbh-version (python-coverage--open-coverage-db coverage-file))
(dbh (car dbh-version))
(stmt (sqlite3-prepare dbh "
SELECT context, hex(numbits)
FROM context
INNER JOIN line_bits ON line_bits.context_id = context.id
INNER JOIN file on line_bits.file_id = file.id
WHERE path = ? AND context IS NOT NULL AND context != '';")))
(sqlite3-bind-text stmt 1 python-file-name)
(let* ((contexts ()))
(while (= sqlite-row (sqlite3-step stmt))
(-let*
(((context hex-numbits) (sqlite3-fetch stmt))
(covered-line-nums (python-coverage--hex-numbits-to-nums hex-numbits)))
(when (cl-intersection line-nums covered-line-nums)
(setq contexts (cons context contexts)))))
(sqlite3-finalize stmt)
(sqlite3-close dbh)
(seq-uniq contexts))))

(defun python-coverage--open-coverage-db (coverage-file)
"Open coverage-file as a SQLite database, check the schema version, returning a 2-list (handle version)"
;; We return the version number because in the future calling functions
;; may need to issue different SQL statements based on this.
(-when-let*
((dbh (sqlite3-open coverage-file sqlite-open-readonly))
(stmt (sqlite3-prepare dbh "SELECT version FROM coverage_schema;")))
(sqlite3-step stmt)
(-let
[(version) (sqlite3-fetch stmt)]
(when (/= version 7)
(message (format "python-coverage might not correctly support the schema version in your .coverage file - version %d. " version)))
(sqlite3-finalize stmt)
(list dbh version))))

(defun python-coverage--get-empty-source-lines ()
(save-excursion
(let ((empty-lines ())
(line-num 1))
(goto-char (point-min))
(while (not (eobp))
(beginning-of-line)
(when (looking-at-p "[[:blank:]]*$")
(setq empty-lines (cons line-num empty-lines)))
(forward-line)
(setq line-num (1+ line-num)))
empty-lines)))

(defun python-coverage--hex-to-bytes (hexstring)
"Convert string containing hex pairs (e.g. \"bc3509\") into vector of integers (bytes) for each pair"
(vconcat (mapcar (lambda (pair)
(string-to-number (concat pair) 16))
(-partition 2 (string-to-list hexstring)))))


(defun python-coverage--numbits-to-nums (numbits)
"Convert vector of integers (bytes) into list of numbers, as per the coveragepy function"
;; Follows the Python version fairly closely for simplicity
(let ((nums ()))

(dotimes (byte-i (length numbits))
(let ((byte (elt numbits byte-i)))
(dotimes (bit-i 8)
(when (> (logand byte (ash 1 bit-i)) 0)
(setq nums (cons (+ (* byte-i 8) bit-i) nums))))))

(reverse nums)))

(defun python-coverage--hex-numbits-to-nums (hex-numbits)
(python-coverage--numbits-to-nums (python-coverage--hex-to-bytes hex-numbits)))

(ert-deftest python-coverage--test-numbits-to-nums ()
;; Used Python version as oracle
(should (equal (python-coverage--hex-numbits-to-nums "DA5BCD70BE1024939024024000000008")
'(1 3 4 6 7 8 9 11 12 14 16 18 19 22 23 28 29 30 33 34 35
36 37 39 44 50 53 56 57 60 63 68 71 74 77 81 94 123))))

;; Internal helpers for handling the coverage XML format

(defun python-coverage--is-xml (file-name)
(with-temp-buffer
(insert-file-contents file-name nil 0 5)
(string= (buffer-substring-no-properties 1 6) "<?xml")))


(defun python-coverage--parse-xml-file (name)
"Parse an XML file NAME."
;; Try to use libxml, and fall back to the slower built-in function.
Expand Down Expand Up @@ -422,7 +595,10 @@ If OUTDATED is non-nil, use a different style."
The EVENT causes the overlays in BUFFER to get refreshed."
(when (buffer-live-p buffer)
(with-current-buffer buffer
(python-coverage-overlay-refresh))))
;; File events for deletion of `.coverage` file can trigger this,
;; in which case overlays will fail. We want to ignore that.
(ignore-errors
(python-coverage-overlay-refresh)))))

;; Internal helpers for flycheck

Expand Down